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Sample GSM401844 Query DataSets for GSM401844
Status Public on Apr 20, 2010
Title UMARY-1584-PONS-CpG
Sample type genomic
 
Source name Human Brain Tissue: PONS
Organism Homo sapiens
Characteristics gender: female
age: 18
pmi: 15
tissuebank: UMARY
prep_hyb_batch: PLATE_W
tissue: pons
Extracted molecule genomic DNA
Extraction protocol Genomic DNA for the Infinium methylation assay was extracted using phenol-chloroform and ethanol precipitation. DNA concentration was determined using a Nanodrop ND-1000 spectrophotometer (Thermo Scientific, Wilmington, DE), and DNA extraction was repeated using a new tissue aliquot for samples with DNA concentration less than 50ng/ul, or with a 260/280 ratio less than 1.7.
Label C-Bio and A-DNP
Label protocol 1ug of genomic DNA underwent bisulfite conversion using the WZ-96 DNA Methylation Kit according to the manufacturer’s protocol (Zymo Research Corp, Orange, CA). Incubation conditions used during conversion were as follows: (95°C for 30 seconds, 50°C for 1 hour) for 16 cycles, hold overnight at 4°C. Unmethylated cytosines were chemically deaminated to uracil in the presence of bisulfite, while methylated cytosines were refractory to the effects of bisulfite and remained as cytosines. Methylation was then detected as a C/T nucleotide polymorphism at each CpG site. After bisulfite conversion, each sample was whole-genome amplified, fragmented, and hybridized to the BeadChip. DNA molecules anneal to locus-specific DNA oligomers.
 
Hybridization protocol Two bead types correspond to each CpG locus, one to the methylated (C) state, and the other to the unmethylated (T) state. After extension, the BeadChip was fluorescently stained.
Scan protocol Illumina Beadstation BeadArray laser confocal scanner to measure the intensities of unmethylated and methylated bead types for each locus.
Description Human Brain Tissue: PONS
Data processing Beadstudio Methylation Module v3.2.0, no normalization (analysis performed on the non-normalized data).
 
Submission date May 11, 2009
Last update date May 15, 2009
Contact name J Raphael Gibbs
E-mail(s) gibbsr@mail.nih.gov
Organization name National Institutue on Aging, NIH
Department Computational Biology Core
Lab Laboratory of Neurogenetics
Street address 35 Convent Drive, Bldg 35/1A1015, MSC3707
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL8490
Series (1)
GSE15745 Abundant Quantitative Trait Loci for CpG Methylation and Expression Across Human Brain Tissues

Data table header descriptions
ID_REF
VALUE Illumina Average Beta
Intensity Illumina Intensity
Detection_Pval Illumina Detection p-value
Avg_NBEADS_A Illumina Average Number Beads A
Avg_NBEADS_B Illumina Average Number Beads B
BEAD_STDERR_A Illumina Beads A Standard Error
BEAD_STDERR_B Illumina Beads B Standard Error
Signal_A Illumina Signal A
Signal_B Illumina Signal B

Data table
ID_REF VALUE Intensity Detection_Pval Avg_NBEADS_A Avg_NBEADS_B BEAD_STDERR_A BEAD_STDERR_B Signal_A Signal_B
cg00000292 0.6653286 15345 3.678E-38 20 18 447.8844 580.9305 5069 10276
cg00002426 0.4759164 6502 3.678E-38 16 17 332.5 412.5 3360 3142
cg00003994 0.03082614 10443 3.678E-38 16 18 714.25 57 10118 325
cg00005847 0.2776168 13361 3.678E-38 24 11 635.8467 262.2995 9624 3737
cg00006414 0.01618159 8799 3.678E-38 17 14 601.4883 18.19017 8655 144
cg00007981 0.0213433 8193 3.678E-38 25 22 645.6 26.8 8016 177
cg00008493 0.9870896 17870 3.678E-38 12 11 22.51666 871.2216 132 17738
cg00008713 0.013009 22346 3.678E-38 20 19 1374.287 33.54102 22054 292
cg00009407 0.03409703 24037 3.678E-38 13 24 1098.861 114.5456 23214 823
cg00010193 0.6365891 37813 3.678E-38 12 18 1911.029 1735.804 13678 24135
cg00011459 0.9555535 10767 3.678E-38 17 18 43.89895 979.1163 383 10384
cg00012199 0.01056803 12012 3.678E-38 24 23 1157.588 12.04332 11884 128
cg00012386 0.01626948 21720 3.678E-38 12 15 2613.376 49.07477 21365 355
cg00012792 0.01500248 28162 3.678E-38 13 21 2887.215 63.23582 27738 424
cg00013618 0.8954994 16120 3.678E-38 10 16 154.3192 2365.067 1595 14525
cg00014085 0.01910055 15554 3.678E-38 20 16 1253.987 47.62825 15255 299
cg00014837 0.9118031 6034 3.678E-38 14 14 62.53913 633.1419 441 5593
cg00015770 0.05829677 22234 3.678E-38 20 17 933.782 93.24403 20932 1302
cg00016968 0.7426976 31773 3.678E-38 16 7 442.75 1896.75 8101 23672
cg00019495 0.1237758 10928 3.678E-38 15 12 1030.988 118.7715 9563 1365

Total number of rows: 27578

Table truncated, full table size 1892 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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